(Reuters) - The U.S. Justice Department said on Friday that its investigation into the handling of rape reports by prosecutors in Missoula, Montana, has found substantial evidence that the county attorney's office discriminates against women.

The 20-page letter caps a nearly two-year inquiry into how the Missoula County Attorney's Office deals with sexual assault. It was made public days after County Attorney Fred Van Valkenburg sued the U.S. Justice Department, accusing its attorneys of overstepping their bounds by trying to oversee local prosecutors.

Among the investigation's findings were that the county attorney's office gave sexual assault of women low priority, failed to properly train its prosecutors and treated victims with disrespect.

In its letter to Van Valkenburg, the Justice Department accused the local prosecutor of failing to cooperate with the probe, including a refusal to provide requested records or access to staff for interviews.

Valkenburg could not be reached for comment after business hours on Friday.

The Justice Department did not announce any actions it was taking in response to the findings but said it hoped the letter would serve as a starting point for talks with the county attorney's office that would avoid protracted litigation.

The Justice Department reached separate agreements last May with the Missoula Police Department and the University of Montana on ways to reform how those two institutions respond to complaints of sex crimes.

The federal investigation stemmed from allegations that the Missoula-based university and local law enforcement had failed to aggressively pursue sexual assault and harassment reports, several of which involved University of Montana football players.

In 2012 the Justice Department announced that it would examine responses by local officials to 80 reported rapes over a three-year period. The U.S. Department of Education, meanwhile, said it would probe whether the university had responded appropriately to at least 11 reported sexual assaults since 2010.

Valkenburg on Tuesday filed a lawsuit in U.S. District Court in Montana against the Justice Department, U.S. Attorney General Eric Holder and others alleging they did not have the authority to investigate or sue him or his office, court records show.

"Those allegations are false, unfounded, and the defendants have exceeded their statutory and constitutional authority," according to the lawsuit.